This algorithm searches for peaks in a dataset. More...

#include <FindPeaks.h>

Inheritance diagram for Mantid::Algorithms::FindPeaks:

Public Member Functions
const std::string	category () const override
	Algorithm's category for identification. More...

	FindPeaks ()
	Constructor. More...

int	getIndex (const HistogramData::HistogramX &vecX, double x)
	needed by FindPeaksBackground More...

const std::string	name () const override
	Algorithm's name. More...

const std::vector< std::string >	seeAlso () const override
	Function to return all of the seeAlso algorithms related to this algorithm. More...

const std::string	summary () const override
	Summary of algorithms purpose. More...

int	version () const override
	Algorithm's version. More...

	~FindPeaks () override=default
	Virtual destructor. More...

Public Member Functions inherited from Mantid::API::Algorithm
	Algorithm ()
	Constructor. More...

	Algorithm (const Algorithm &)=delete

Algorithm &	operator= (const Algorithm &)=delete

	~Algorithm () override
	Virtual destructor. More...

void	initialize () override
	Initialization method invoked by the framework. More...

bool	execute () override final
	The actions to be performed by the algorithm on a dataset. More...

void	addTimer (const std::string &name, const Kernel::time_point_ns &begin, const Kernel::time_point_ns &end)

void	executeAsChildAlg () override
	Execute as a Child Algorithm. More...

std::map< std::string, std::string >	validateInputs () override
	Perform validation of ALL the input properties of the algorithm. More...

ExecutionState	executionState () const override
	Gets the current execution state. More...

ResultState	resultState () const override
	Gets the current result State. More...

bool	isInitialized () const override
	Has the Algorithm already been initialized. More...

bool	isExecuted () const override
	Has the Algorithm already been executed successfully. More...

bool	isRunning () const override
	True if the algorithm is running. More...

bool	isReadyForGarbageCollection () const override
	True if the algorithm is ready for garbage collection. More...

bool	isChild () const override
	To query whether algorithm is a child. More...

void	setChild (const bool isChild) override
	To set whether algorithm is a child. More...

void	enableHistoryRecordingForChild (const bool on) override
	Change the state of the history recording flag. More...

bool	isRecordingHistoryForChild ()

void	setAlwaysStoreInADS (const bool doStore) override
	Do we ALWAYS store in the AnalysisDataService? This is set to true for python algorithms' child algorithms. More...

bool	getAlwaysStoreInADS () const override
	Returns true if we always store in the AnalysisDataService. More...

void	setRethrows (const bool rethrow) override
	Set whether the algorithm will rethrow exceptions. More...

Poco::ActiveResult< bool >	executeAsync () override
	Asynchronous execution. More...

void	addObserver (const Poco::AbstractObserver &observer) const override
	Add an observer for a notification. More...

void	removeObserver (const Poco::AbstractObserver &observer) const override
	Remove an observer. More...

void	cancel () override
	Raises the cancel flag. More...

bool	getCancel () const
	Returns the cancellation state. More...

Kernel::Logger &	getLogger () const
	Returns a reference to the logger. More...

void	setLogging (const bool value) override
	Logging can be disabled by passing a value of false. More...

bool	isLogging () const override
	returns the status of logging, True = enabled More...

void	setLoggingOffset (const int value) override
	gets the logging priority offset More...

int	getLoggingOffset () const override
	returns the logging priority offset More...

void	setAlgStartupLogging (const bool enabled) override
	disable Logging of start and end messages More...

bool	getAlgStartupLogging () const override
	get the state of Logging of start and end messages More...

void	setChildStartProgress (const double startProgress) const override
	setting the child start progress More...

void	setChildEndProgress (const double endProgress) const override
	setting the child end progress More...

std::string	toString () const override
	Serialize an object to a string. More...

::Json::Value	toJson () const override
	Serialize an object to a json object. More...

virtual std::shared_ptr< Algorithm >	createChildAlgorithm (const std::string &name, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true, const int &version=-1)
	Create a Child Algorithm. More...

void	setupAsChildAlgorithm (const Algorithm_sptr &algorithm, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true)
	Setup algorithm as child algorithm. More...

void	trackAlgorithmHistory (std::shared_ptr< AlgorithmHistory > parentHist)
	set whether we wish to track the child algorithm's history and pass it the parent object to fill. More...

void	findWorkspaces (WorkspaceVector &workspaces, unsigned int direction, bool checkADS=false) const
	Populate lists of the workspace properties for a given direction (InOut workspaces are included in both input/output) More...

virtual bool	checkGroups ()
	Check the input workspace properties for groups. More...

virtual bool	processGroups ()
	Process WorkspaceGroup inputs. More...

void	copyNonWorkspaceProperties (IAlgorithm *alg, int periodNum)
	Copy all the non-workspace properties from this to alg. More...

const Parallel::Communicator &	communicator () const
	Returns a const reference to the (MPI) communicator of the algorithm. More...

void	setCommunicator (const Parallel::Communicator &communicator)
	Sets the (MPI) communicator of the algorithm. More...

void	declareProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override
	Add a property to the list of managed properties. More...

void	declareOrReplaceProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override
	Add or replace property in the list of managed properties. More...

void	resetProperties () override
	Reset property values back to initial values (blank or default values) More...

void	setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
	Set the ordered list of properties by one string of values, separated by semicolons. More...

void	setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
	Sets all the declared properties from a json object. More...

void	setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >()) override
	Sets all the declared properties from a string. More...

void	setPropertyValue (const std::string &name, const std::string &value) override
	Set the value of a property by string N.B. More...

void	setPropertyValueFromJson (const std::string &name, const Json::Value &value) override
	Set the value of a property by Json::Value object. More...

void	setPropertyOrdinal (const int &index, const std::string &value) override
	Set the value of a property by an index N.B. More...

virtual void	copyPropertiesFrom (const Algorithm &alg)
	Make m_properties point to the same PropertyManager as alg.m_properties. More...

bool	existsProperty (const std::string &name) const override
	Checks whether the named property is already in the list of managed property. More...

bool	validateProperties () const override
	Validates all the properties in the collection. More...

size_t	propertyCount () const override
	Count the number of properties under management. More...

std::string	getPropertyValue (const std::string &name) const override
	Get the value of a property as a string. More...

const std::vector< Kernel::Property * > &	getProperties () const override
	Get the list of managed properties. More...

std::vector< std::string >	getDeclaredPropertyNames () const noexcept override
	Return the list of declared property names. More...

TypedValue	getProperty (const std::string &name) const override
	Get the value of a property. More...

std::string	asString (bool withDefaultValues=false) const override
	Return the property manager serialized as a string. More...

::Json::Value	asJson (bool withDefaultValues=false) const override
	Return the property manager serialized as a json object. More...

bool	isDefault (const std::string &name) const

void	removeProperty (const std::string &name, const bool delproperty=true) override
	Removes the property from management. More...

std::unique_ptr< Kernel::Property >	takeProperty (const size_t index) override
	Removes the property from management and returns a pointer to it. More...

void	clear () override
	Clears all properties under management. More...

void	afterPropertySet (const std::string &) override
	Override this method to perform a custom action right after a property was set. More...

void	filterByTime (const Types::Core::DateAndTime &, const Types::Core::DateAndTime &) override

void	splitByTime (std::vector< Kernel::SplittingInterval > &, std::vector< Kernel::PropertyManager * >) const override

void	filterByProperty (const Kernel::TimeSeriesProperty< bool > &, const std::vector< std::string > &) override

Kernel::Property *	getPointerToProperty (const std::string &name) const override
	Get a property by name. More...

Kernel::Property *	getPointerToPropertyOrdinal (const int &index) const override
	Get a property by an index. More...

virtual void	declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
	Function to declare properties (i.e. store them) More...

template<typename T >
void	declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
	Add a property of the template type to the list of managed properties. More...

template<typename T >
void	declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
	Add a property to the list of managed properties with no validator. More...

template<typename T >
void	declareProperty (const std::string &name, T value, const unsigned int direction)
	Add a property of the template type to the list of managed properties. More...

void	declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

void	declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

void	declareProperty (const std::string &name, const char *value, const unsigned int direction)
	Add a property of string type to the list of managed properties. More...

const std::string	category () const override
	function to return a category of the algorithm. More...

const std::vector< std::string >	categories () const override
	Function to return all of the categories that contain this algorithm. More...

const std::string	categorySeparator () const override
	Function to return the separator token for the category string. More...

const std::vector< std::string >	seeAlso () const override
	Function to return all of the seeAlso (these are not validated) algorithms related to this algorithm.A default implementation is provided. More...

const std::string	alias () const override
	function to return any aliases to the algorithm; A default implementation is provided More...

const std::string	aliasDeprecated () const override
	Expiration date (in ISO8601 format) for the algorithm aliases; default implementation for no expiration date. More...

const std::string	helpURL () const override
	function to return URL for algorithm documentation; A default implementation is provided. More...

template<typename T , typename = typename std::enable_if<std::is_convertible<T , MatrixWorkspace >::value>::type>
std::tuple< std::shared_ptr< T >, Indexing::SpectrumIndexSet >	getWorkspaceAndIndices (const std::string &name) const

template<typename T1 , typename T2 , typename = typename std::enable_if<std::is_convertible<T1 , MatrixWorkspace >::value>::type, typename = typename std::enable_if<std::is_convertible<T2 , std::string >::value \|\| std::is_convertible<T2 , std::vector<int64_t> >::value>::type>
void	setWorkspaceInputProperties (const std::string &name, const std::shared_ptr< T1 > &wksp, IndexType type, const T2 &list)

template<typename T1 , typename T2 , typename = typename std::enable_if<std::is_convertible<T1 , MatrixWorkspace >::value>::type, typename = typename std::enable_if<std::is_convertible<T2 , std::string >::value \|\| std::is_convertible<T2 , std::vector<int64_t> >::value>::type>
void	setWorkspaceInputProperties (const std::string &name, const std::string &wsName, IndexType type, const T2 &list)

const std::string	workspaceMethodName () const override

const std::vector< std::string >	workspaceMethodOn () const override

const std::string	workspaceMethodInputProperty () const override

AlgorithmID	getAlgorithmID () const override
	Algorithm ID. More...

virtual void	addObserver (const Poco::AbstractObserver &observer) const =0
	Add an observer for a notification. More...

virtual const std::string	alias () const =0
	function to return any aliases of the algorithm. More...

virtual const std::string	aliasDeprecated () const =0
	Expiration date (in ISO8601 format) for the algorithm aliases. Empty if no expiration date. More...

virtual void	cancel ()=0
	Raises the cancel flag. More...

virtual const std::vector< std::string >	categories () const =0
	Function to return all of the categories that contain this algorithm. More...

virtual const std::string	category () const =0
	function to return a category of the algorithm. More...

virtual const std::string	categorySeparator () const =0
	Function to return the separator token for the category string. More...

virtual void	enableHistoryRecordingForChild (const bool on)=0
	If true history will be recorded for a child. More...

virtual bool	execute ()=0
	System execution. More...

virtual void	executeAsChildAlg ()=0
	Execute as a Child Algorithm, with try/catch. More...

virtual Poco::ActiveResult< bool >	executeAsync ()=0
	Asynchronous execution of the algorithm. More...

virtual ExecutionState	executionState () const =0
	Gets the current execution state. More...

virtual AlgorithmID	getAlgorithmID () const =0
	Algorithm ID. More...

virtual bool	getAlgStartupLogging () const =0
	get the state of Logging of start and end messages More...

virtual bool	getAlwaysStoreInADS () const =0
	To query whether the output is stored in the analysis data service. More...

virtual int	getLoggingOffset () const =0
	returns the logging priority offset More...

virtual const std::string	helpURL () const =0
	function to return an optional URL for documentation. More...

virtual void	initialize ()=0
	Initialization method invoked by the framework. More...

virtual bool	isChild () const =0
	To query whether algorithm is a child. Default to false. More...

virtual bool	isExecuted () const =0
	Check whether the algorithm has been executed sucessfully. More...

virtual bool	isInitialized () const =0
	Check whether the algorithm is initialized properly. More...

virtual bool	isLogging () const =0
	returns the status of logging, True = enabled More...

virtual bool	isReadyForGarbageCollection () const =0
	True if the algorithm is ready for garbage collection. More...

virtual bool	isRunning () const =0
	True if the algorithm is running. More...

virtual const std::string	name () const =0
	function to return a name of the algorithm, must be overridden in all algorithms More...

virtual void	removeObserver (const Poco::AbstractObserver &observer) const =0
	Remove an observer. More...

virtual ResultState	resultState () const =0
	Gets the currnet result State. More...

virtual const std::vector< std::string >	seeAlso () const =0
	Function to return all of the seeAlso algorithms related to this algorithm. More...

virtual void	setAlgStartupLogging (const bool enabled)=0
	disable Logging of start and end messages More...

virtual void	setAlwaysStoreInADS (const bool doStore)=0
	Set whether we always store the output in the analysis data service. More...

virtual void	setChild (const bool isChild)=0
	To set whether algorithm is a child. More...

virtual void	setChildEndProgress (const double endProgress) const =0
	setting the child end progress More...

virtual void	setChildStartProgress (const double startProgress) const =0
	setting the child start progress More...

virtual void	setLogging (const bool value)=0
	Logging can be disabled by passing a value of false. More...

virtual void	setLoggingOffset (const int value)=0
	gets the logging priority offset More...

virtual void	setRethrows (const bool rethrow)=0
	To query whether an algorithm should rethrow exceptions when executing. More...

virtual const std::string	summary () const =0
	function returns a summary message that will be displayed in the default GUI, and in the help. More...

virtual ::Json::Value	toJson () const =0
	Serialize an algorithm as Json. More...

virtual std::string	toString () const =0
	Serialize an algorithm. More...

virtual std::map< std::string, std::string >	validateInputs ()=0
	Method checking errors on ALL the inputs, before execution. More...

virtual int	version () const =0
	function to return a version of the algorithm, must be overridden in all algorithms More...

Algorithms As Methods
Public Member Functions inherited from Mantid::Kernel::IPropertyManager
virtual ::Json::Value	asJson (bool withDefaultValues=false) const =0
	Return the property manager serialized as a json object. More...

virtual std::string	asString (bool withDefaultValues=false) const =0
	Return the property manager serialized as a string. More...

virtual void	declareOrReplaceProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
	Function to declare properties (i.e. store them) More...

void	declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

void	declareProperty (const std::string &name, const char *value, const unsigned int direction)
	Add a property of string type to the list of managed properties. More...

void	declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

template<typename T >
void	declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
	Add a property to the list of managed properties with no validator. More...

template<typename T >
void	declareProperty (const std::string &name, T value, const unsigned int direction)
	Add a property of the template type to the list of managed properties. More...

template<typename T >
void	declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
	Add a property of the template type to the list of managed properties. More...

virtual void	declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
	Function to declare properties (i.e. store them) More...

virtual bool	existsProperty (const std::string &name) const =0
	Checks whether the named property is already in the list of managed property. More...

virtual void	filterByProperty (const TimeSeriesProperty< bool > &, const std::vector< std::string > &)=0

virtual void	filterByTime (const Types::Core::DateAndTime &, const Types::Core::DateAndTime &)=0

virtual std::vector< std::string >	getDeclaredPropertyNames () const noexcept=0
	Get the list of managed property names. More...

virtual Property *	getPointerToProperty (const std::string &name) const =0
	Get a pointer to property by name. More...

virtual const std::vector< Property * > &	getProperties () const =0
	Get the list of managed properties. More...

std::vector< Property * >	getPropertiesInGroup (const std::string &group) const
	Get the list of managed properties in a given group. More...

virtual TypedValue	getProperty (const std::string &name) const =0
	Get the value of a property. More...

virtual std::string	getPropertyValue (const std::string &name) const =0
	Get the value of a property as a string. More...

virtual size_t	propertyCount () const =0
	Returns the number of properties under management. More...

virtual void	removeProperty (const std::string &name, const bool delproperty=true)=0
	Removes the property from management. More...

virtual void	resetProperties ()=0

virtual void	setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0
	Sets all the properties from a json object. More...

virtual void	setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0
	Sets all properties from a string. More...

virtual void	setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >())=0
	Sets all the declared properties from a string. More...

IPropertyManager *	setProperty (const std::string &name, const char *value)
	Specialised version of setProperty template method to handle const char *. More...

IPropertyManager *	setProperty (const std::string &name, const std::string &value)
	Specialised version of setProperty template method to handle std::string. More...

template<typename T >
IPropertyManager *	setProperty (const std::string &name, const T &value)
	Templated method to set the value of a PropertyWithValue. More...

template<typename T >
IPropertyManager *	setProperty (const std::string &name, std::unique_ptr< T > value)
	Templated method to set the value of a PropertyWithValue from a std::unique_ptr. More...

void	setPropertyGroup (const std::string &name, const std::string &group)
	Set the group for a given property. More...

virtual void	setPropertyOrdinal (const int &index, const std::string &value)=0
	Set the value of a property by an index. More...

void	setPropertySettings (const std::string &name, std::unique_ptr< IPropertySettings > settings)

virtual void	setPropertyValue (const std::string &name, const std::string &value)=0
	Sets property value from a string. More...

virtual void	setPropertyValueFromJson (const std::string &name, const Json::Value &value)=0
	Sets property value from a Json::Value. More...

virtual void	splitByTime (std::vector< SplittingInterval > &, std::vector< PropertyManager * >) const =0

virtual std::unique_ptr< Property >	takeProperty (const size_t index)=0
	Removes the property from management and returns a pointer to it. More...

void	updatePropertyValues (const IPropertyManager &other)
	Update values of the existing properties. More...

virtual bool	validateProperties () const =0
	Validates all the properties in the collection. More...

virtual	~IPropertyManager ()=default

Private Member Functions
void	addInfoRow (const size_t spectrum, const API::IPeakFunction_const_sptr &peakfunction, const API::IBackgroundFunction_sptr &bkgdfunction, const bool isoutputraw, const double mincost)
	Add a new row in output TableWorkspace containing information of the fitted peak+background. More...

void	addNonFitRecord (const size_t spectrum, const double centre)
	Add the fit record (failure) to output workspace. More...

std::vector< HistogramData::Histogram >	calculateSecondDifference (const API::MatrixWorkspace_const_sptr &input)
	Methods searving for findPeaksUsingMariscotti() More...

void	calculateStandardDeviation (const API::MatrixWorkspace_const_sptr &input, std::vector< HistogramData::Histogram > &smoothed, const int &w)
	Calculates the statistical error on the smoothed data. More...

double	callFitPeak (const API::MatrixWorkspace_sptr &dataws, int wsindex, const API::IPeakFunction_sptr &peakfunction, const API::IBackgroundFunction_sptr &backgroundfunction, const std::vector< double > &vec_fitwindow, const std::vector< double > &vec_peakrange, int minGuessFWHM, int maxGuessFWHM, int guessedFWHMStep, int estBackResult=0)
	Fit peak by calling 'FitPeak'. More...

long long	computePhi (const int &w) const
	Calculates the coefficient phi which goes into the calculation of the error on the smoothed data Uses Mariscotti equation (11). More...

void	createFunctions ()
	Create peak and background functions. More...

void	estimateBackground (const HistogramData::HistogramX &X, const HistogramData::HistogramY &Y, const size_t i_min, const size_t i_max, std::vector< double > &vecbkgdparvalues)
	Estimate background of a given range. More...

std::string	estimatePeakParameters (const HistogramData::HistogramX &vecX, const HistogramData::HistogramY &vecY, size_t i_min, size_t i_max, const std::vector< double > &vecbkgdparvalues, size_t &iobscentre, double &height, double &fwhm, double &leftfwhm, double &rightfwhm)
	Estimate peak parameters. More...

void	estimatePeakRange (const HistogramData::HistogramX &vecX, size_t i_centre, size_t i_min, size_t i_max, const double &leftfwhm, const double &rightfwhm, std::vector< double > &vecpeakrange)
	Estimate peak range based on background peak parameter. More...

void	exec () override
	Execute the findPeaks algorithm. More...

int	findPeakBackground (const API::MatrixWorkspace_sptr &input, int spectrum, size_t i_min, size_t i_max, std::vector< double > &vecBkgdParamValues, std::vector< double > &vecpeakrange)
	Find peak background. More...

void	findPeaksGivenStartingPoints (const std::vector< double > &peakcentres, const std::vector< double > &fitwindows)
	Find peaks according to given peak positions. More...

void	findPeaksUsingMariscotti ()
	Find peaks by searching peak position using Mariscotti algorithm. More...

void	fitPeakGivenFWHM (const API::MatrixWorkspace_sptr &input, const int spectrum, const double center_guess, const int fitWidth, const bool hasleftpeak, const double leftpeakcentre, const bool hasrightpeak, const double rightpeakcentre)
	Fit peak by given/guessed FWHM. More...

void	fitPeakHighBackground (const API::MatrixWorkspace_sptr &input, const size_t spectrum, int i_centre, int i_min, int i_max, double &in_bg0, double &in_bg1, double &in_bg2, int i_peakmin, int i_peakmax)

void	fitPeakInWindow (const API::MatrixWorkspace_sptr &input, const int spectrum, const double centre_guess, const double xmin, const double xmax)
	Fit peak confined in a given window (x-min, x-max) More...

void	fitPeakOneStep (const API::MatrixWorkspace_sptr &input, const int spectrum, const int &i0, const int &i2, const int &i4, const double &in_bg0, const double &in_bg1, const double &in_bg2)

void	fitSinglePeak (const API::MatrixWorkspace_sptr &input, const int spectrum, const int i_min, const int i_max, const int i_centre)
	Fit peak: this is a basic peak fit function as a root function for all different type of user input. More...

void	generateOutputPeakParameterTable ()
	Generate a table workspace for output peak parameters. More...

std::vector< double >	getStartingBkgdValues ()

std::vector< double >	getStartingPeakValues ()
	Get the peak parameter values from m_peakFunction and output to a list in the same order of m_peakParameterNames. More...

void	init () override
	Initialize and declare properties. More...

void	processAlgorithmProperties ()
	Process algorithm's properties. More...

void	smoothData (std::vector< HistogramData::Histogram > &histograms, const int w, const int g_z)
	Smooth data for Mariscotti. More...

Private Attributes
API::IBackgroundFunction_sptr	m_backgroundFunction

std::string	m_backgroundType

size_t	m_bkgdOrder

std::vector< std::string >	m_bkgdParameterNames

std::size_t	m_centreIndex

std::string	m_costFunction

API::MatrixWorkspace_sptr	m_dataWS
	workspace to check for peaks More...

std::vector< API::IFunction_sptr >	m_fitFunctions

bool	m_highBackground
	flag for find relatively weak peak in high More...

Indexing::SpectrumIndexSet	m_indexSet
	list of workspace indicies to check More...

int	m_inputPeakFWHM
	holder for the requested peak FWHM More...

double	m_leastMaxObsY
	Minimum value of peak's observed maximum Y value. More...

int	m_maxGuessedPeakWidth

int	m_minGuessedPeakWidth

double	m_minHeight
	Minimum peak height. More...

std::string	m_minimizer

std::size_t	m_numTableParams
	parameters or effective (centre, width, height) More...

API::ITableWorkspace_sptr	m_outPeakTableWS
	Storage of the peak data. More...

API::IPeakFunction_sptr	m_peakFunction

std::string	m_peakFuncType

std::vector< size_t >	m_peakLeftIndexes

std::vector< std::string >	m_peakParameterNames

double	m_peakPositionTolerance

std::vector< size_t >	m_peakRightIndexes

std::unique_ptr< API::Progress >	m_progress = nullptr
	Progress reporting. More...

bool	m_rawPeaksTable
	background More...

int	m_stepGuessedPeakWidth

bool	m_useObsCentre
	Start values. More...

bool	m_usePeakPositionTolerance

std::vector< double >	m_vecFitWindows

std::vector< double >	m_vecPeakCentre

Static Private Attributes
static const int	g_z = 5
	The number of smoothing iterations. More...

Additional Inherited Members
Public Types inherited from Mantid::API::Algorithm
using	WorkspaceVector = std::vector< std::shared_ptr< Workspace > >

Static Public Member Functions inherited from Mantid::API::Algorithm
static IAlgorithm_sptr	fromString (const std::string &input)
	De-serialize an object from a string. More...

static IAlgorithm_sptr	fromJson (const Json::Value &input)
	De-serialize an object from a Json. More...

static IAlgorithm_sptr	fromHistory (const AlgorithmHistory &history)
	Construct an object from a history entry. More...

Public Attributes inherited from Mantid::API::Algorithm
bool	calledByAlias = false
	Flag to indicate if the algorithm is called by its alias. More...

Protected Member Functions inherited from Mantid::API::ParallelAlgorithm
Parallel::ExecutionMode	getParallelExecutionMode (const std::map< std::string, Parallel::StorageMode > &storageModes) const override
	Get correct execution mode based on input storage modes for an MPI run. More...

	~ParallelAlgorithm ()=default

Protected Member Functions inherited from Mantid::API::Algorithm
void	exec (Parallel::ExecutionMode executionMode)
	Runs the algorithm with the specified execution mode. More...

virtual void	execDistributed ()
	Runs the algorithm in `distributed` execution mode. More...

virtual void	execMasterOnly ()
	Runs the algorithm in `master-only` execution mode. More...

virtual const std::string	workspaceMethodOnTypes () const
	Returns a semi-colon separated list of workspace types to attach this algorithm. More...

void	cacheWorkspaceProperties ()
	Go through the properties and cache the input/output workspace properties for later use. More...

void	cacheInputWorkspaceHistories ()
	Cache the histories of any input workspaces so they can be copied over after algorithm completion. More...

void	setExecutionState (const ExecutionState state)
	Sets the current execution state. More...

void	setResultState (const ResultState state)
	Sets the result execution state. More...

void	store ()
	Stores any output workspaces into the AnalysisDataService. More...

void	progress (double p, const std::string &msg="", double estimatedTime=0.0, int progressPrecision=0)
	Sends ProgressNotification. More...

void	interruption_point ()
	This is called during long-running operations, and check if the algorithm has requested that it be cancelled. More...

Poco::NotificationCenter &	notificationCenter () const
	Return a reference to the algorithm's notification dispatcher. More...

void	handleChildProgressNotification (const Poco::AutoPtr< ProgressNotification > &pNf)
	Observation slot for child algorithm progress notification messages, these are scaled and then signalled for this algorithm. More...

const Poco::AbstractObserver &	progressObserver () const
	Return a reference to the algorithm's object that is reporting progress. More...

bool	isWorkspaceProperty (const Kernel::Property *const prop) const
	checks the property is a workspace property More...

bool	trackingHistory ()
	get whether we are tracking the history for this algorithm, More...

virtual void	fillHistory ()
	Copy workspace history for input workspaces to output workspaces and record the history for ths algorithm. More...

virtual void	setOtherProperties (IAlgorithm *alg, const std::string &propertyName, const std::string &propertyValue, int periodNum)
	Virtual method to set the non workspace properties for this algorithm. More...

template<typename T , const int AllowedIndexTypes = static_cast<int>(IndexType::WorkspaceIndex), typename... WSPropArgs, typename = typename std::enable_if<std::is_convertible<T , MatrixWorkspace >::value>::type>
void	declareWorkspaceInputProperties (const std::string &propertyName, const std::string &doc, WSPropArgs &&...wsPropArgs)

Protected Member Functions inherited from Mantid::Kernel::IPropertyManager
virtual void	afterPropertySet (const std::string &)
	Override this method to perform a custom action right after a property was set. More...

virtual void	clear ()=0
	Clears all properties under management. More...

virtual Property *	getPointerToPropertyOrdinal (const int &index) const =0
	Get a property by an index. More...

template<typename T >
T	getValue (const std::string &name) const
	Templated method to get the value of a property. More...

template<>
MANTID_KERNEL_DLL PropertyManager_sptr	getValue (const std::string &name) const

template<>
MANTID_KERNEL_DLL PropertyManager_const_sptr	getValue (const std::string &name) const

Static Protected Member Functions inherited from Mantid::API::Algorithm
template<typename NumT >
static bool	isEmpty (const NumT toCheck)
	checks that the value was not set by users, uses the value in empty double/int. More...

Protected Attributes inherited from Mantid::API::Algorithm
std::atomic< bool >	m_cancel
	Set to true to stop execution. More...

std::atomic< bool >	m_parallelException
	Set if an exception is thrown, and not caught, within a parallel region. More...

std::vector< IWorkspaceProperty * >	m_inputWorkspaceProps
	All the WorkspaceProperties that are Input or InOut. Set in execute() More...

std::shared_ptr< AlgorithmHistory >	m_history
	Pointer to the history for the algorithm being executed. More...

Kernel::Logger	m_log
	Logger for this algorithm. More...

Kernel::Logger &	g_log

std::shared_ptr< AlgorithmHistory >	m_parentHistory
	Pointer to the parent history object (if set) More...

std::vector< WorkspaceVector >	m_unrolledInputWorkspaces
	One vector of workspaces for each input workspace property. More...

size_t	m_groupSize
	Size of the group(s) being processed. More...

bool	m_usingBaseProcessGroups = false
	distinguish between base processGroups() and overriden/algorithm specific versions More...

Static Protected Attributes inherited from Mantid::API::Algorithm
static size_t	g_execCount = 0
	Counter to keep track of algorithm execution order. More...

Detailed Description

This algorithm searches for peaks in a dataset.

The method used is detailed in: M.A.Mariscotti, NIM 50 (1967) 309.

Required Properties:

InputWorkspace - The name of the Workspace to search for peaks.
PeaksList - The name of the TableWorkspace in which to store the list of peaks found.

Optional Properties:

fwhm - The number of points covered on average by the fwhm of a peak (default 7)
Tolerance - Sets the strictness desired in meeting the conditions on peak candidates (default 4, Mariscotti recommended 2)
WorkspaceIndex - The spectrum to search for peaks. Will search all spectra if absent.

Author: Russell Taylor, Tessella Support Services plc

Date: 25/11/2008

Definition at line 50 of file FindPeaks.h.

Constructor & Destructor Documentation

◆ FindPeaks()

Mantid::Algorithms::FindPeaks::FindPeaks ( )

Constructor.

Definition at line 48 of file FindPeaks.cpp.

◆ ~FindPeaks()

Mantid::Algorithms::FindPeaks::~FindPeaks ( )

overridedefault

Virtual destructor.

Member Function Documentation

◆ addInfoRow()

void Mantid::Algorithms::FindPeaks::addInfoRow	(	const size_t	spectrum,
		const API::IPeakFunction_const_sptr &	peakfunction,
		const API::IBackgroundFunction_sptr &	bkgdfunction,
		const bool	isoutputraw,
		const double	mincost
	)

private

Add a new row in output TableWorkspace containing information of the fitted peak+background.

Add a row to the output table workspace.

Parameters

spectrum	:: spectrum number
peakfunction	:: peak function
bkgdfunction	:: background function
isoutputraw	:: flag to output raw function parameters
mincost	Chi2 value for this set of parameters
mincost	:: minimum/best cost function value

Definition at line 1291 of file FindPeaks.cpp.

References Mantid::Kernel::Logger::debug(), Mantid::API::Algorithm::g_log, height, and m_outPeakTableWS.

Referenced by fitSinglePeak().

◆ addNonFitRecord()

void Mantid::Algorithms::FindPeaks::addNonFitRecord	(	const size_t	spectrum,
		const double	centre
	)

private

Add the fit record (failure) to output workspace.

Parameters

spectrum	:: spectrum where the peak is
centre	:: position of the peak centre

Definition at line 1358 of file FindPeaks.cpp.

References Mantid::API::Algorithm::g_log, Mantid::Kernel::Logger::information(), m_centreIndex, m_numTableParams, and m_outPeakTableWS.

Referenced by findPeaksGivenStartingPoints(), fitPeakInWindow(), and fitSinglePeak().

◆ calculateSecondDifference()

std::vector< Histogram > Mantid::Algorithms::FindPeaks::calculateSecondDifference ( const API::MatrixWorkspace_const_sptr & input )

private

Methods searving for findPeaksUsingMariscotti()

Calculates the second difference of the data (Y values) in a workspace.

Done according to equation (3) in Mariscotti: \( S_i = N_{i+1} - 2N_i + N_{i+1} \). In the output workspace, the 2nd difference is in Y, X is unchanged and E is zero.

Parameters

input :: The workspace to calculate the second difference of

Returns: A workspace containing the second difference

Definition at line 583 of file FindPeaks.cpp.

References m_indexSet, and Mantid::Geometry::Y.

Referenced by findPeaksUsingMariscotti().

◆ calculateStandardDeviation()

void Mantid::Algorithms::FindPeaks::calculateStandardDeviation	(	const API::MatrixWorkspace_const_sptr &	input,
		std::vector< HistogramData::Histogram > &	smoothed,
		const int &	w
	)

private

Calculates the statistical error on the smoothed data.

Uses Mariscotti equation (11), amended to use errors of input data rather than sqrt(Y).

Parameters

input	:: The input data to the algorithm
smoothed	:: The smoothed dataBackgroud type is not supported in FindPeak.cpp
w	:: The value of w (the size of the smoothing 'window')

Exceptions

std::invalid_argument if w is greater than 19

Definition at line 628 of file FindPeaks.cpp.

References computePhi(), g_z, and m_indexSet.

Referenced by findPeaksUsingMariscotti().

◆ callFitPeak()

double Mantid::Algorithms::FindPeaks::callFitPeak	(	const API::MatrixWorkspace_sptr &	dataws,
		int	wsindex,
		const API::IPeakFunction_sptr &	peakfunction,
		const API::IBackgroundFunction_sptr &	backgroundfunction,
		const std::vector< double > &	vec_fitwindow,
		const std::vector< double > &	vec_peakrange,
		int	minGuessFWHM,
		int	maxGuessFWHM,
		int	guessedFWHMStep,
		int	estBackResult = `0`
	)

private

Fit peak by calling 'FitPeak'.

Fit a single peak function with background by calling algorithm callFitPeak.

Definition at line 1408 of file FindPeaks.cpp.

Referenced by fitSinglePeak().

◆ category()

const std::string Mantid::Algorithms::FindPeaks::category ( ) const

inlineoverridevirtual

Algorithm's category for identification.

Implements Mantid::API::IAlgorithm.

Definition at line 65 of file FindPeaks.h.

◆ computePhi()

long long Mantid::Algorithms::FindPeaks::computePhi ( const int & w ) const

private

Calculates the coefficient phi which goes into the calculation of the error on the smoothed data Uses Mariscotti equation (11).

Pinched from the GeneralisedSecondDifference code. Can return a very big number, hence the type.

Parameters

w	The value of w (the size of the smoothing 'window')

Returns: The value of phi(g_z,w)

Definition at line 653 of file FindPeaks.cpp.

References Mantid::Kernel::Logger::debug(), Mantid::Kernel::delta, Mantid::API::Algorithm::g_log, g_z, index, and Mantid::Geometry::m.

Referenced by calculateStandardDeviation().

◆ createFunctions()

void Mantid::Algorithms::FindPeaks::createFunctions ( )

private

Create peak and background functions.

Create functions and related variables.

Definition at line 1381 of file FindPeaks.cpp.

References Mantid::API::Algorithm::g_log, Mantid::Kernel::Logger::information(), Mantid::Kernel::SingletonHolder< T >::Instance(), m_backgroundFunction, m_backgroundType, m_bkgdOrder, m_bkgdParameterNames, m_peakFunction, m_peakFuncType, and m_peakParameterNames.

Referenced by exec().

◆ estimateBackground()

void Mantid::Algorithms::FindPeaks::estimateBackground	(	const HistogramData::HistogramX &	X,
		const HistogramData::HistogramY &	Y,
		const size_t	i_min,
		const size_t	i_max,
		std::vector< double > &	vecbkgdparvalues
	)

private

Estimate background of a given range.

Estimate background parameter values and peak range The background to estimate is a linear background.

Assuming the first and last data points cannot be a major part of the peak unless the fit window is too small.

Parameters

X	:: vec for X
Y	:: vec for Y
i_min	:: index of minimum in X to estimate background
i_max	:: index of maximum in X to estimate background
vecbkgdparvalues	:: vector of double for a0, a1 and a2 of background

Definition at line 1184 of file FindPeaks.cpp.

References m_bkgdOrder, MAGICNUMBER, Mantid::Geometry::X, and Mantid::Geometry::Y.

Referenced by fitSinglePeak().

◆ estimatePeakParameters()

std::string Mantid::Algorithms::FindPeaks::estimatePeakParameters	(	const HistogramData::HistogramX &	vecX,
		const HistogramData::HistogramY &	vecY,
		size_t	i_min,
		size_t	i_max,
		const std::vector< double > &	vecbkgdparvalues,
		size_t &	iobscentre,
		double &	height,
		double &	fwhm,
		double &	leftfwhm,
		double &	rightfwhm
	)

private

Estimate peak parameters.

Estimate peak parameters Assumption: pure peak workspace with background removed (but it might not be true...)

Parameters

vecX	:: vector of X-axis
vecY	:: vector of Y-axis
i_min	:: start
i_max	:: end
vecbkgdparvalues	:: vector of background parameters (a0, a1, a2)
iobscentre	:: (output) bin index of estimated peak centre (maximum position)
height	:: (output) estimated maximum
fwhm	:: (output) estimated fwhm
leftfwhm	:: (output) left side fhwm
rightfwhm	:: (output) right side fwhm

Returns: error mesage

Definition at line 1055 of file FindPeaks.cpp.

References Mantid::API::Algorithm::g_log, height, Mantid::Kernel::Logger::information(), m_minHeight, and Mantid::Geometry::x.

Referenced by fitSinglePeak().

◆ estimatePeakRange()

void Mantid::Algorithms::FindPeaks::estimatePeakRange	(	const HistogramData::HistogramX &	vecX,
		size_t	i_centre,
		size_t	i_min,
		size_t	i_max,
		const double &	leftfwhm,
		const double &	rightfwhm,
		std::vector< double > &	vecpeakrange
	)

private

Estimate peak range based on background peak parameter.

Estimate peak range according to observed peak parameters and (linear) background.

Definition at line 1237 of file FindPeaks.cpp.

References getIndex().

Referenced by fitSinglePeak().

◆ exec()

void Mantid::Algorithms::FindPeaks::exec ( )

overrideprivatevirtual

Execute the findPeaks algorithm.

Implements Mantid::API::Algorithm.

Definition at line 156 of file FindPeaks.cpp.

References createFunctions(), findPeaksGivenStartingPoints(), findPeaksUsingMariscotti(), Mantid::API::Algorithm::g_log, generateOutputPeakParameterTable(), Mantid::Kernel::Logger::information(), m_outPeakTableWS, m_usePeakPositionTolerance, m_vecFitWindows, m_vecPeakCentre, processAlgorithmProperties(), and Mantid::Kernel::IPropertyManager::setProperty().

◆ findPeakBackground()

int Mantid::Algorithms::FindPeaks::findPeakBackground	(	const API::MatrixWorkspace_sptr &	input,
		int	spectrum,
		size_t	i_min,
		size_t	i_max,
		std::vector< double > &	vecBkgdParamValues,
		std::vector< double > &	vecpeakrange
	)

private

Find peak background.

Find peak background given a certain range by calling algorithm "FindPeakBackground".

Todo:: Allow setting of fitresult. Currently, fitresult is left deliberately hidden by creating a new variable here with the same name. This should be fixed but it causes different behaviour which breaks several unit tests. The issue to deal with this is #13950. Other related issues are #13667, #15978 and #19773.

Definition at line 957 of file FindPeaks.cpp.

References Mantid::API::Algorithm::createChildAlgorithm(), Mantid::Kernel::Logger::debug(), Mantid::API::Algorithm::g_log, Mantid::Kernel::Logger::information(), and m_backgroundType.

Referenced by fitSinglePeak().

◆ findPeaksGivenStartingPoints()

void Mantid::Algorithms::FindPeaks::findPeaksGivenStartingPoints	(	const std::vector< double > &	peakcentres,
		const std::vector< double > &	fitwindows
	)

private

Find peaks according to given peak positions.

Find the start positions to fit peaks with given estimated peak centres.

Parameters

peakcentres	:: vector of the center x-positions specified to perform fits.
fitwindows	:: vector of windows around each peak. Otherwise, windows will be determined automatically.

Definition at line 310 of file FindPeaks.cpp.

References addNonFitRecord(), Mantid::Kernel::Logger::debug(), fitPeakGivenFWHM(), fitPeakInWindow(), Mantid::API::Algorithm::g_log, Mantid::Kernel::Logger::information(), m_dataWS, m_indexSet, m_inputPeakFWHM, m_progress, and Mantid::Kernel::Logger::warning().

Referenced by exec().

◆ findPeaksUsingMariscotti()

void Mantid::Algorithms::FindPeaks::findPeaksUsingMariscotti ( )

private

Find peaks by searching peak position using Mariscotti algorithm.

Use the Mariscotti method to find the start positions and fit gaussian peaks.

Definition at line 395 of file FindPeaks.cpp.

References calculateSecondDifference(), calculateStandardDeviation(), Mantid::Kernel::Logger::debug(), fitSinglePeak(), Mantid::API::Algorithm::g_log, g_z, Mantid::API::Algorithm::getProperty(), m_dataWS, m_indexSet, m_inputPeakFWHM, m_progress, smoothData(), and tolerance.

Referenced by exec().

◆ fitPeakGivenFWHM()

void Mantid::Algorithms::FindPeaks::fitPeakGivenFWHM	(	const API::MatrixWorkspace_sptr &	input,
		const int	wsIndex,
		const double	center_guess,
		const int	fitWidth,
		const bool	hasleftpeak,
		const double	leftpeakcentre,
		const bool	hasrightpeak,
		const double	rightpeakcentre
	)

private

Fit peak by given/guessed FWHM.

Attempts to fit a candidate peak given a center and width guess.

(This is not the CORE fit peak method)

Parameters

input	:: The input workspace
wsIndex	:: The workspace index of the peak
center_guess	:: A guess of the X-value of the center of the peak, in whatever units of the X-axis of the workspace.
fitWidth	:: A guess of the full-width-half-max of the peak, in # of bins.
hasleftpeak	:: flag to show that there is a specified peak to its left
leftpeakcentre	:: centre of left peak if existed
hasrightpeak	:: flag to show that there is a specified peak to its right
rightpeakcentre	:: centre of the right peak if existed

Definition at line 755 of file FindPeaks.cpp.

References fitSinglePeak(), Mantid::API::Algorithm::g_log, getIndex(), and Mantid::Kernel::Logger::information().

Referenced by findPeaksGivenStartingPoints().

◆ fitPeakHighBackground()

void Mantid::Algorithms::FindPeaks::fitPeakHighBackground	(	const API::MatrixWorkspace_sptr &	input,
		const size_t	spectrum,
		int	i_centre,
		int	i_min,
		int	i_max,
		double &	in_bg0,
		double &	in_bg1,
		double &	in_bg2,
		int	i_peakmin,
		int	i_peakmax
	)

private

◆ fitPeakInWindow()

void Mantid::Algorithms::FindPeaks::fitPeakInWindow	(	const API::MatrixWorkspace_sptr &	input,
		const int	wsIndex,
		const double	centre_guess,
		const double	xmin,
		const double	xmax
	)

private

Fit peak confined in a given window (x-min, x-max)

Attempts to fit a candidate peak with a given window of where peak resides.

Parameters

input	The input workspace
wsIndex	The workspace index of the peak
centre_guess	:: Channel number of peak candidate i0 - the higher side of the peak (right side)
xmin	Minimum x value to find the peak
xmax	Maximum x value to find the peak

Definition at line 813 of file FindPeaks.cpp.

References addNonFitRecord(), fitSinglePeak(), Mantid::API::Algorithm::g_log, getIndex(), Mantid::Kernel::Logger::information(), and Mantid::Kernel::Logger::warning().

Referenced by findPeaksGivenStartingPoints().

◆ fitPeakOneStep()

void Mantid::Algorithms::FindPeaks::fitPeakOneStep	(	const API::MatrixWorkspace_sptr &	input,
		const int	spectrum,
		const int &	i0,
		const int &	i2,
		const int &	i4,
		const double &	in_bg0,
		const double &	in_bg1,
		const double &	in_bg2
	)

private

References Mantid::Algorithms::PeakParameterHelper::estimatePeakParameters().

◆ fitSinglePeak()

void Mantid::Algorithms::FindPeaks::fitSinglePeak	(	const API::MatrixWorkspace_sptr &	input,
		const int	spectrum,
		const int	i_min,
		const int	i_max,
		const int	i_centre
	)

private

Fit peak: this is a basic peak fit function as a root function for all different type of user input.

Fit a single peak This is the fundametary peak fit function used by all kinds of input.

Definition at line 855 of file FindPeaks.cpp.

References addInfoRow(), addNonFitRecord(), callFitPeak(), Mantid::Kernel::Logger::debug(), estimateBackground(), estimatePeakParameters(), estimatePeakRange(), fabs, findPeakBackground(), Mantid::API::Algorithm::g_log, Mantid::Kernel::Logger::information(), m_backgroundFunction, m_bkgdOrder, m_leastMaxObsY, m_maxGuessedPeakWidth, m_minGuessedPeakWidth, m_minHeight, m_peakFunction, m_peakPositionTolerance, m_rawPeaksTable, m_stepGuessedPeakWidth, m_useObsCentre, m_usePeakPositionTolerance, and Mantid::Kernel::Logger::warning().

Referenced by findPeaksUsingMariscotti(), fitPeakGivenFWHM(), and fitPeakInWindow().

◆ generateOutputPeakParameterTable()

void Mantid::Algorithms::FindPeaks::generateOutputPeakParameterTable ( )

private

Generate a table workspace for output peak parameters.

Definition at line 263 of file FindPeaks.cpp.

References m_backgroundFunction, m_bkgdParameterNames, m_centreIndex, m_numTableParams, m_outPeakTableWS, m_peakFunction, m_peakFuncType, m_peakParameterNames, and m_rawPeaksTable.

Referenced by exec().

◆ getIndex()

int Mantid::Algorithms::FindPeaks::getIndex	(	const HistogramData::HistogramX &	vecX,
		double	x
	)

needed by FindPeaksBackground

Find the index of a value (or nearest) in a given the X data.

Parameters

vecX	:: vector
x	:: value to search

Returns: index of x in vector

Definition at line 702 of file FindPeaks.cpp.

References Mantid::API::Algorithm::g_log, index, Mantid::Kernel::Logger::warning(), and Mantid::Geometry::x.

Referenced by estimatePeakRange(), Mantid::Algorithms::FindPeakBackground::findWindowIndex(), fitPeakGivenFWHM(), and fitPeakInWindow().

◆ getStartingBkgdValues()

std::vector< double > Mantid::Algorithms::FindPeaks::getStartingBkgdValues ( )

private

◆ getStartingPeakValues()

std::vector< double > Mantid::Algorithms::FindPeaks::getStartingPeakValues ( )

private

Get the peak parameter values from m_peakFunction and output to a list in the same order of m_peakParameterNames.

Definition at line 1452 of file FindPeaks.cpp.

References m_peakFunction.

◆ init()

void Mantid::Algorithms::FindPeaks::init ( )

overrideprivatevirtual

Initialize and declare properties.

Implements Mantid::API::Algorithm.

Definition at line 60 of file FindPeaks.cpp.

References Mantid::API::Algorithm::declareProperty(), Mantid::EMPTY_DBL(), Mantid::EMPTY_INT(), Mantid::Kernel::Direction::Input, Mantid::Kernel::SingletonHolder< T >::Instance(), and Mantid::Kernel::Direction::Output.

◆ name()

const std::string Mantid::Algorithms::FindPeaks::name ( ) const

inlineoverridevirtual

Algorithm's name.

Implements Mantid::API::Algorithm.

Definition at line 57 of file FindPeaks.h.

◆ processAlgorithmProperties()

void Mantid::Algorithms::FindPeaks::processAlgorithmProperties ( )

private

Process algorithm's properties.

Definition at line 191 of file FindPeaks.cpp.

References Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), Mantid::API::Algorithm::isEmpty(), m_backgroundType, m_costFunction, m_dataWS, m_highBackground, m_indexSet, m_inputPeakFWHM, m_leastMaxObsY, m_maxGuessedPeakWidth, m_minGuessedPeakWidth, m_minHeight, m_minimizer, m_peakFuncType, m_peakPositionTolerance, m_rawPeaksTable, m_stepGuessedPeakWidth, m_useObsCentre, m_usePeakPositionTolerance, m_vecFitWindows, m_vecPeakCentre, and Mantid::Kernel::Logger::warning().

Referenced by exec().

◆ seeAlso()

const std::vector< std::string > Mantid::Algorithms::FindPeaks::seeAlso ( ) const

inlineoverridevirtual

Function to return all of the seeAlso algorithms related to this algorithm.

Implements Mantid::API::IAlgorithm.

Definition at line 63 of file FindPeaks.h.

◆ smoothData()

void Mantid::Algorithms::FindPeaks::smoothData	(	std::vector< HistogramData::Histogram > &	histograms,
		const int	w,
		const int	g_z
	)

private

Smooth data for Mariscotti.

Parameters

histograms	:: Vector of histograms to be smoothed (inplace).
w	:: The number of data points which should contribute to each smoothed point
g_z	:: The number of smoothing steps given by g_z (should be 5)

Definition at line 612 of file FindPeaks.cpp.

References g_z, and Mantid::Algorithms::smooth().

Referenced by findPeaksUsingMariscotti().

◆ summary()

const std::string Mantid::Algorithms::FindPeaks::summary ( ) const

inlineoverridevirtual

Summary of algorithms purpose.

Implements Mantid::API::Algorithm.

Definition at line 59 of file FindPeaks.h.

◆ version()

int Mantid::Algorithms::FindPeaks::version ( ) const

inlineoverridevirtual

Algorithm's version.

Implements Mantid::API::Algorithm.

Definition at line 62 of file FindPeaks.h.

Member Data Documentation

◆ g_z

const int Mantid::Algorithms::FindPeaks::g_z = 5

staticprivate

The number of smoothing iterations.

Set to 5, the optimum value according to Mariscotti.

Definition at line 156 of file FindPeaks.h.

Referenced by calculateStandardDeviation(), computePhi(), findPeaksUsingMariscotti(), and smoothData().

◆ m_backgroundFunction

API::IBackgroundFunction_sptr Mantid::Algorithms::FindPeaks::m_backgroundFunction

private

Definition at line 182 of file FindPeaks.h.

Referenced by createFunctions(), fitSinglePeak(), and generateOutputPeakParameterTable().

◆ m_backgroundType

std::string Mantid::Algorithms::FindPeaks::m_backgroundType

private

Definition at line 175 of file FindPeaks.h.

Referenced by createFunctions(), findPeakBackground(), and processAlgorithmProperties().

◆ m_bkgdOrder

size_t Mantid::Algorithms::FindPeaks::m_bkgdOrder

private

Definition at line 152 of file FindPeaks.h.

Referenced by createFunctions(), estimateBackground(), and fitSinglePeak().

◆ m_bkgdParameterNames

std::vector<std::string> Mantid::Algorithms::FindPeaks::m_bkgdParameterNames

private

Definition at line 151 of file FindPeaks.h.

Referenced by createFunctions(), and generateOutputPeakParameterTable().

◆ m_centreIndex

std::size_t Mantid::Algorithms::FindPeaks::m_centreIndex

private

Definition at line 173 of file FindPeaks.h.

Referenced by addNonFitRecord(), and generateOutputPeakParameterTable().

◆ m_costFunction

std::string Mantid::Algorithms::FindPeaks::m_costFunction

private

Definition at line 197 of file FindPeaks.h.

Referenced by callFitPeak(), and processAlgorithmProperties().

◆ m_dataWS

API::MatrixWorkspace_sptr Mantid::Algorithms::FindPeaks::m_dataWS

private

workspace to check for peaks

Definition at line 164 of file FindPeaks.h.

Referenced by findPeaksGivenStartingPoints(), findPeaksUsingMariscotti(), and processAlgorithmProperties().

◆ m_fitFunctions

std::vector<API::IFunction_sptr> Mantid::Algorithms::FindPeaks::m_fitFunctions

private

Definition at line 192 of file FindPeaks.h.

◆ m_highBackground

bool Mantid::Algorithms::FindPeaks::m_highBackground

private

flag for find relatively weak peak in high

Definition at line 168 of file FindPeaks.h.

Referenced by callFitPeak(), and processAlgorithmProperties().

◆ m_indexSet

Indexing::SpectrumIndexSet Mantid::Algorithms::FindPeaks::m_indexSet

private

list of workspace indicies to check

Definition at line 166 of file FindPeaks.h.

Referenced by calculateSecondDifference(), calculateStandardDeviation(), findPeaksGivenStartingPoints(), findPeaksUsingMariscotti(), and processAlgorithmProperties().

◆ m_inputPeakFWHM

int Mantid::Algorithms::FindPeaks::m_inputPeakFWHM

private

holder for the requested peak FWHM

Definition at line 165 of file FindPeaks.h.

Referenced by findPeaksGivenStartingPoints(), findPeaksUsingMariscotti(), and processAlgorithmProperties().

◆ m_leastMaxObsY

double Mantid::Algorithms::FindPeaks::m_leastMaxObsY

private

Minimum value of peak's observed maximum Y value.

Definition at line 202 of file FindPeaks.h.

Referenced by fitSinglePeak(), and processAlgorithmProperties().

◆ m_maxGuessedPeakWidth

int Mantid::Algorithms::FindPeaks::m_maxGuessedPeakWidth

private

Definition at line 186 of file FindPeaks.h.

Referenced by fitSinglePeak(), and processAlgorithmProperties().

◆ m_minGuessedPeakWidth

int Mantid::Algorithms::FindPeaks::m_minGuessedPeakWidth

private

Definition at line 185 of file FindPeaks.h.

Referenced by fitSinglePeak(), and processAlgorithmProperties().

◆ m_minHeight

double Mantid::Algorithms::FindPeaks::m_minHeight

private

Minimum peak height.

Definition at line 200 of file FindPeaks.h.

Referenced by estimatePeakParameters(), fitSinglePeak(), and processAlgorithmProperties().

◆ m_minimizer

std::string Mantid::Algorithms::FindPeaks::m_minimizer

private

Definition at line 196 of file FindPeaks.h.

Referenced by callFitPeak(), and processAlgorithmProperties().

◆ m_numTableParams

std::size_t Mantid::Algorithms::FindPeaks::m_numTableParams

private

parameters or effective (centre, width, height)

Definition at line 172 of file FindPeaks.h.

Referenced by addNonFitRecord(), and generateOutputPeakParameterTable().

◆ m_outPeakTableWS

API::ITableWorkspace_sptr Mantid::Algorithms::FindPeaks::m_outPeakTableWS

private

Storage of the peak data.

Definition at line 159 of file FindPeaks.h.

Referenced by addInfoRow(), addNonFitRecord(), exec(), and generateOutputPeakParameterTable().

◆ m_peakFunction

API::IPeakFunction_sptr Mantid::Algorithms::FindPeaks::m_peakFunction

private

Definition at line 183 of file FindPeaks.h.

Referenced by callFitPeak(), createFunctions(), fitSinglePeak(), generateOutputPeakParameterTable(), and getStartingPeakValues().

◆ m_peakFuncType

std::string Mantid::Algorithms::FindPeaks::m_peakFuncType

private

Definition at line 174 of file FindPeaks.h.

Referenced by createFunctions(), generateOutputPeakParameterTable(), and processAlgorithmProperties().

◆ m_peakLeftIndexes

std::vector<size_t> Mantid::Algorithms::FindPeaks::m_peakLeftIndexes

private

Definition at line 193 of file FindPeaks.h.

◆ m_peakParameterNames

std::vector<std::string> Mantid::Algorithms::FindPeaks::m_peakParameterNames

private

Definition at line 150 of file FindPeaks.h.

Referenced by createFunctions(), and generateOutputPeakParameterTable().

◆ m_peakPositionTolerance

double Mantid::Algorithms::FindPeaks::m_peakPositionTolerance

private

Definition at line 190 of file FindPeaks.h.

Referenced by fitSinglePeak(), and processAlgorithmProperties().

◆ m_peakRightIndexes

std::vector<size_t> Mantid::Algorithms::FindPeaks::m_peakRightIndexes

private

Definition at line 194 of file FindPeaks.h.

◆ m_progress

std::unique_ptr<API::Progress> Mantid::Algorithms::FindPeaks::m_progress = nullptr

private

Progress reporting.

Definition at line 161 of file FindPeaks.h.

Referenced by findPeaksGivenStartingPoints(), and findPeaksUsingMariscotti().

◆ m_rawPeaksTable

bool Mantid::Algorithms::FindPeaks::m_rawPeaksTable

private

background

flag for whether the output is the raw peak

Definition at line 170 of file FindPeaks.h.

Referenced by fitSinglePeak(), generateOutputPeakParameterTable(), and processAlgorithmProperties().

◆ m_stepGuessedPeakWidth

int Mantid::Algorithms::FindPeaks::m_stepGuessedPeakWidth

private

Definition at line 187 of file FindPeaks.h.

Referenced by fitSinglePeak(), and processAlgorithmProperties().

◆ m_useObsCentre

bool Mantid::Algorithms::FindPeaks::m_useObsCentre

private

Start values.

Definition at line 205 of file FindPeaks.h.

Referenced by fitSinglePeak(), and processAlgorithmProperties().

◆ m_usePeakPositionTolerance

bool Mantid::Algorithms::FindPeaks::m_usePeakPositionTolerance

private

Definition at line 189 of file FindPeaks.h.

Referenced by exec(), fitSinglePeak(), and processAlgorithmProperties().

◆ m_vecFitWindows

std::vector<double> Mantid::Algorithms::FindPeaks::m_vecFitWindows

private

Definition at line 179 of file FindPeaks.h.

Referenced by exec(), and processAlgorithmProperties().

◆ m_vecPeakCentre

std::vector<double> Mantid::Algorithms::FindPeaks::m_vecPeakCentre

private

Definition at line 178 of file FindPeaks.h.

Referenced by exec(), and processAlgorithmProperties().

The documentation for this class was generated from the following files:

Framework/Algorithms/inc/MantidAlgorithms/FindPeaks.h
Framework/Algorithms/src/FindPeaks.cpp

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FindPeaks()

◆ ~FindPeaks()

Member Function Documentation

◆ addInfoRow()

◆ addNonFitRecord()

◆ calculateSecondDifference()

◆ calculateStandardDeviation()

◆ callFitPeak()

◆ category()

◆ computePhi()

◆ createFunctions()

◆ estimateBackground()

◆ estimatePeakParameters()

◆ estimatePeakRange()

◆ exec()

◆ findPeakBackground()

◆ findPeaksGivenStartingPoints()

◆ findPeaksUsingMariscotti()

◆ fitPeakGivenFWHM()

◆ fitPeakHighBackground()

◆ fitPeakInWindow()

◆ fitPeakOneStep()

◆ fitSinglePeak()

◆ generateOutputPeakParameterTable()

◆ getIndex()

◆ getStartingBkgdValues()

◆ getStartingPeakValues()

◆ init()

◆ name()

◆ processAlgorithmProperties()

◆ seeAlso()

◆ smoothData()

◆ summary()

◆ version()

Member Data Documentation

◆ g_z

◆ m_backgroundFunction

◆ m_backgroundType

◆ m_bkgdOrder

◆ m_bkgdParameterNames

◆ m_centreIndex

◆ m_costFunction

◆ m_dataWS

◆ m_fitFunctions

◆ m_highBackground

◆ m_indexSet

◆ m_inputPeakFWHM

◆ m_leastMaxObsY

◆ m_maxGuessedPeakWidth

◆ m_minGuessedPeakWidth

◆ m_minHeight

◆ m_minimizer

◆ m_numTableParams

◆ m_outPeakTableWS

◆ m_peakFunction

◆ m_peakFuncType

◆ m_peakLeftIndexes

◆ m_peakParameterNames

◆ m_peakPositionTolerance

◆ m_peakRightIndexes

◆ m_progress

◆ m_rawPeaksTable

◆ m_stepGuessedPeakWidth

◆ m_useObsCentre

◆ m_usePeakPositionTolerance

◆ m_vecFitWindows

◆ m_vecPeakCentre